Environmentally benign-solvent free plasma process is employed to produce nanostructured PFDA-co-DEGDME amphiphilic coatings via plasma co-polymerisation of 1H,1H,2H,2H-perfluorodecyl acrylate (PFDA) and diethyleneglycol dimethyl ether (DEGDME) precursors in a low pressure-RF-inductively excited tubular plasma reactor using argon as a carrier gas. The plasma-polymerised coatings are characterised by Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), field emission scanning electron microscopy (FESEM), atomic force microscopy (AFM) and contact angle measurements. PFDA-co-DEGDME coatings with varying chemical environments and morphologies are achieved by varying the plasma parameters such as, continuous wave (CW) and pulse modulated (PM) plasma mode, and plasma deposition time. Plasma polymerised PFDAco- DEGDME coatings are found to exhibit a switching property in terms of wettability, i.e., from hydrophobic to hydrophilic and vice versa, in response to the contacting environment. Quartz crystal microbalance (QCM) is used to study the adhesion of two model proteins, namely, human serum albumin (HSA) and fibrinogen (FGN) in continuous flow conditions, which reveals the protein repellent, i.e., anti-biofouling characteristics of the PFDAco- DEGDME amphiphilic coatings.